The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I would imagine that pricing for the 4000 runs may be higher for the first 6-12 months.

The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I would imagine that pricing for the 4000 runs may be higher for the first 6-12 months.

Yes, I think maybe the main benefit from the 3000/4000 over a 2500-1T running v4 chemistry would be less worries about overclustering a flow cell. And that is big--on a psychological level. But I think most cores have systems in place that either make this rare or just leave it up to the customers to send correctly titred libraries.

I know nobody here cares about microarrays (nor should we?), but I think Illumina deserves some serious mad-scientist points for the NextSeq 550. If I'm understanding correctly, they've made a microarray adapter that fits in the flow-cell slot, and are reading it with the same scanner. More innovation than I'd expect from a company with a secure monopoly.
Maybe this is an attempt to wean the last few stragglers off arrays and get them into sequencing?

They had the HiScanSQ that did arrays plus sequencing and that was quickly discontinued. Asked an Illumina employee about it and he said it seemed like they were trying to make peanut butter and jelly again - he couldn't figure out the logic in it either.

It's cheaper than the NextSeq 500 and iScan combined, so might be useful for research labs looking for a sequencer and array as well or those doing scanning as followups. Seems very niche though.

Looks like most of the points on the latest Illumina tech have been covered in this thread. A few others points that I haven't seen covered yet:

- HiSeq 3000 will cost around the same as HiSeq 2500 v4.
- HiSeq 3000 is upgradeable to HiSeq 4000 (the HiSeq v4 upgrade was only available on instruments that shipped after 2013).
- You can upgrade from X Five to X Ten...just buy more instruments, but at the lower $1M/instrument cost.
- Illumina is going to start bundling library prep and cluster reagents on the X series.
- X series is still only for whole human WGS...likely to focus battle w/ the BGI / CG WGS instrument release later this year or a good excuse to release more patterned flow cell models....

As a platform that regularly handles sequencing service listings and orders, Genohub collects a lot of information on price and changes in price once a new instrument is released. In general, we've noticed what others have posted in this thread, price per Gb is rarely more competitive immediately after an instrument is released. There are still many providers offering excellent turnaround times and prices on HiSeq services that will continue to be competitive even after we have our first HiSeq 3000/4000 listed on Genohub.

In the sense that a 3000 will produce about the same amount of sequence per unit time as a 2500-1T. Also in the sense that Illumina priced the 3000 at the current 2500 price.
But in the sense that the 2500 is a 2 flow cell instrument it would be replaced by the 4000 as a 3000 has only one flow cell.

Quote:

3. rapid mode will not be supported by either the HiSeq3000/4000.

I only see this from Jay Flatley to support your statement:

Quote:

There will be a number of customers who remain on the 2500, however, due to the use of validated workflows or the importance of access to rapid run mode and longer reads.

But this doesn't imply that rapid chemistry will never be available on the 3000/4000, does it?

In the sense that a 3000 will produce about the same amount of sequence per unit time as a 2500-1T. Also in the sense that Illumina priced the 3000 at the current 2500 price.

But in the sense that the 2500 is a 2 flow cell instrument it would be replaced by the 4000 as a 3000 has only one flow cell.

And in the sense that the people who bought the 2500 in Q4 will be potentially be offered a 3000 and not a 4000. I'm entertaining the Illumina POV here...

Quote:

But this doesn't imply that rapid chemistry will never be available on the 3000/4000, does it?

Correct, it doesn't, so yes I'm reading between the lines here...

I'd say given the push for the NextSeqDx, and dropping the HiSeq2500 for 510(k) clearance, it makes less sense to introduce rapid mode capacity (or even maintain for the 2500) for the 3000/4000 when there is a NextSeq500 that is being pushed as a product.

Besides, I don't think that ordered clustering is something that can be pushed in the same kind of way any time soon...